A2A: a platform for research in biomedical literature search

• Published in: BMC bioinformatics 2020-12, Vol.21 (Suppl 19), p.572-572, Article 572
• Main Authors: Rybinski, Maciej, Karimi, Sarvnaz, Nguyen, Vincent, Paris, Cecile
• Format: Article
• Language: English
• Subjects: Access to information; Biomedical Research; Biomedical search; Clinical decision support; Collections; Data entry; Databases, Factual; Evaluation; Experiments; Genomics; Humans; Information processing; Information retrieval; Information Storage and Retrieval - methods; Life sciences; Medical research; Medical Subject Headings; Medicine; Medicine, Experimental; Methods; Precision medicine; Query expansion; Query formulation; Query processing; Research methodology; Researchers; Retrieval performance measures; Search engines; Search methods; Software; Technology application; User interface; Web applications
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-020-03894-8

Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published literature, given a query. However, they are limited in how users can control the processing of queries and articles-or as we call them documents-by the search engine. To give this control to both biomedical researchers and computer scientists working in biomedical information retrieval, we introduce a public online tool for searching over biomedical literature. Our setup is guided by the NIST setup of the relevant TREC evaluation tasks in genomics, clinical decision support, and precision medicine. To provide benchmark results for some of the most common biomedical information retrieval strategies, such as querying MeSH subject headings with a specific weight or querying over the title of the articles only, we present our evaluations on public datasets. Our experiments report well-known information retrieval metrics such as precision at a cutoff of ranked documents. We introduce the A2A search and benchmarking tool which is publicly available for the researchers who want to explore different search strategies over published biomedical literature. We outline several query formulation strategies and present their evaluations with known human judgements for a large pool of topics, from genomics to precision medicine.